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Methods. 2019 Apr 15;159-160:4-22. doi: 10.1016/j.ymeth.2019.03.009. Epub 2019 Mar 16.

Role of integrative structural biology in understanding transcriptional initiation.

Author information

1
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
2
Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756 CNRS & IP, Paris, France.
3
Department of Biological Sciences, Birkbeck University of London, Institute of Structural and Molecular Biology, London, United Kingdom. Electronic address: p.robinson@mail.cryst.bbk.ac.uk.

Abstract

Integrative structural biology combines data from multiple experimental techniques to generate complete structural models for the biological system of interest. Most commonly cross-linking data sets are employed alongside electron microscopy maps, crystallographic structures, and other data by computational methods that integrate all known information and produce structural models at a level of resolution that is appropriate to the input data. The precision of these modelled solutions is limited by the sparseness of cross-links observed, the length of the cross-linking reagent, the ambiguity arisen from the presence of multiple copies of the same protein, and structural and compositional heterogeneity. In recent years integrative structural biology approaches have been successfully applied to a range of RNA polymerase II complexes. Here we will provide a general background to integrative structural biology, a description of how it should be practically implemented and how it has furthered our understanding of the biology of large transcriptional assemblies. Finally, in the context of recent breakthroughs in microscope and direct electron detector technology, where increasingly EM is capable of resolving structural features directly without the aid of other structural techniques, we will discuss the future role of integrative structural techniques.

KEYWORDS:

Computational molecular modelling; Cross-linking mass spectrometry; Cryo-EM; Integrative structural determination; Multi-subunit complex architecture; RNA polymerase II; Transcriptional initiation machinery

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